Hmm.. that's tough.
343 Guilty Spark has to be on my list. It should be on everyone's who encountered the Flood for the first time on it.
Uprising(Halo 2)
The Maw (Halo 2)
Floodgate(Halo 3)
The Covenant(Halo 3)

Silent Cartographer was the first i had ever played, but my favorite ones are Halo (Halo 3) with legendary ending, The Ark (Halo 3), Cortana (Halo 3), 343 Guilty Spark (Halo CE), High Charity (Halo 2), The Great Journey (Halo 2), The Package (Halo: Reach), Lone Wolf (Halo: Reach/The death of Noble 6)
And i f****** hate The Libary on Legendary that took me some hours.